***Mother and child stool bacteriomes: links to maternal gestational diabetes and atopic dermatitis in 1–2-years-old children***
Authors: Kristi Alnek a, Anu Bärenson a,b, Oliver Aasmets c, Helis Janson a, Ija Talja a,d, Brita Laht a, 
Tamara Vorobjova a, Anne Kirss e, Ondrej Cinek f, Raivo Uibo a, Aili Tagoma a, HEDIMED Investigator group
a Department of Immunology, Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia
b Children’s Clinic of Tartu University Hospital, Tartu, Estonia
c Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia 
d Present address - United Laboratories of Tartu University Hospital, Tartu, Estonia
e Women’s Clinic of Tartu University Hospital, Tartu, Estonia 
f Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic

#corresponding author: Kristi Alnek
#contact information: kristi.alnek@ut.ee

**General information**
This file contains reads based on ASV data of the gut bacteriomes of mothers with and 
without GDM and those of their children (1-2 years old) resulting from the pregnancies.

**Methodology**
A fragment spanning variable regions 3 and 4 of the 16S bacterial ribosomal 
gene was amplified with AccuPrime Pfx SuperMix (Invitrogen). The libraries were 
sequenced on a MiSeq instrument using a Reagent Kit v2 (Illumina, San Diego, CA,
USA). Samples were amplified and sequenced in technical duplicates that shared 
no sequencing index. In addition, they were sequenced with several DNA replicates 
from the Microbial Mock Community (HM-276D; BEI Resources, Manassas, VA, USA) and 
with negative controls (PCR water as a template). 
 
The raw data were downloaded as demultiplexed fastq files with trimmed adapters. 
The primary bioinformatics analysis was performed using the DADA2 pipeline 
(version 1.16), as advised by the software developers, with the trimming of the 
first 12 bases and the following parameters: maximum number of ambiguous bases = 0; 
maximum numbers of expected errors for forward and reverse reads = 2 and 3, respectively; 
and maximum number of truncates on quality = 2. The sequences were taxonomically 
classified using the SILVA database (version 138). From the DADA2 pipeline–produced 
amplicon sequence variants (ASVs) table and taxonomy, failed reactions (those with fewer 
than 1000 reads per replicate) were first removed. Negative controls were then checked for 
the absence of a significant signal, and the mock community positions were assessed for 
agreement with their declared content. 
 
**abbreviated words**
ASV - amplicon sequence variants 
 
***Sharing and Access information***
This data is made public for other researchers to use in their own work under CC-BY-SA.